Input Specification if Pre-Existing MetaPhlAn Files

6. I already have MetaPhlAn output. Can I start HUMAnN 3.0 with the MetaPhlAn output?
Yes, use the --taxonomic-profile bugs_list.tsv option

But, what should the user specify for --input which is mandatory? bowtie2out isn’t a valid option unlike it is for MetaPhlAn 3.

--input would still be your FASTQ file (reads) in this case: providing MetaPhlAn output to HUMAnN just allows you to skip the first step in which HUMAnN would otherwise run MetaPhlAn for you.

Ah, I see. Do you plan to include some short vignettes in future that demonstrate steps end-to-end?

We have a HUMAnN tutorial here?

This covers the default workflow and a few common follow-up steps. Special options (like bypassing MetaPhlAn) are described in the manual but omitted from the Tutorial in the interest of brevity.

Ah, thanks for the link. I was only reading the HUMAnN repository but it is in biobakery.